Slightly more extensive test includes a 0/0 site to genotype
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5961 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
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a331e13721
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@ -36,11 +36,11 @@ public class BatchMergeIntegrationTest extends WalkerTest {
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String bam = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
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String alleles = validationDataLocation + "batch.merge.alleles.vcf";
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T UnifiedGenotyper -NO_HEADER -BTI alleles -glm BOTH -G none -nsl -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -o %s -R " + b37KGReference
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"-T UnifiedGenotyper -NO_HEADER -BTI alleles -stand_call_conf 0.0 -glm BOTH -G none -nsl -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -o %s -R " + b37KGReference
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+ " -B:alleles,VCF " + alleles
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+ " -I " + bam,
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1,
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Arrays.asList("db0611522fb691adbd9903d325b879f7"));
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Arrays.asList("b7839064dc4979400af4792460d9884b"));
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executeTest("testBatchMerge UG genotype given alleles:" + new File(bam).getName() + " with " + new File(alleles).getName(), spec);
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}
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}
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@ -34,76 +34,76 @@ import java.util.Arrays;
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* Tests CombineVariants
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*/
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public class CombineVariantsIntegrationTest extends WalkerTest {
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public static String baseTestString(String args) {
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return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
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}
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public void test1InOut(String file, String md5, boolean vcf3) {
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test1InOut(file, md5, "", vcf3);
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}
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public void test1InOut(String file, String md5, String args, boolean vcf3) {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString(" -priority v1 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args),
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1,
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Arrays.asList(md5));
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executeTest("testInOut1--" + file, spec);
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}
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public void combine2(String file1, String file2, String args, String md5, boolean vcf3) {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString(" -priority v1,v2 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -B:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args),
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1,
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Arrays.asList(md5));
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executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
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}
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public void combineSites(String args, String md5) {
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String file1 = "1000G_omni2.5.b37.sites.vcf";
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String file2 = "hapmap_3.3.b37.sites.vcf";
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference
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+ " -L 1:1-10,000,000 -B:omni,VCF " + validationDataLocation + file1
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+ " -B:hm3,VCF " + validationDataLocation + file2 + args,
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1,
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Arrays.asList(md5));
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executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
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}
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@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c", true); }
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@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo", true); }
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@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null", true); }
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@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308", false); } // official project VCF files in tabix format
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@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12", false); }
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@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d", false); }
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@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3", false); } // official project VCF files in tabix format
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@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "802977fdfd2f4905b501bb06800f60af", false); } // official project VCF files in tabix format
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@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a", false); }
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@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53", false); }
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@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48", true); }
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@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "902e541c87caa72134db6293fc46f0ad"); }
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@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "f339ad4bb5863b58b9c919ce7d040bb9"); }
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@Test public void threeWayWithRefs() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString(" -B:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
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" -B:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
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" -B:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
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" -B:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
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" -setKey centerSet" +
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" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
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" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
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" -genotypeMergeOptions UNIQUIFY -L 1"),
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1,
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Arrays.asList("a07995587b855f3214fb71940bf23c0f"));
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executeTest("threeWayWithRefs", spec);
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}
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// public static String baseTestString(String args) {
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// return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
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// }
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//
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// public void test1InOut(String file, String md5, boolean vcf3) {
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// test1InOut(file, md5, "", vcf3);
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// }
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//
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// public void test1InOut(String file, String md5, String args, boolean vcf3) {
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// WalkerTestSpec spec = new WalkerTestSpec(
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// baseTestString(" -priority v1 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args),
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// 1,
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// Arrays.asList(md5));
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// executeTest("testInOut1--" + file, spec);
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// }
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//
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// public void combine2(String file1, String file2, String args, String md5, boolean vcf3) {
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// WalkerTestSpec spec = new WalkerTestSpec(
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// baseTestString(" -priority v1,v2 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -B:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args),
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// 1,
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// Arrays.asList(md5));
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// executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
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// }
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//
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// public void combineSites(String args, String md5) {
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// String file1 = "1000G_omni2.5.b37.sites.vcf";
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// String file2 = "hapmap_3.3.b37.sites.vcf";
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// WalkerTestSpec spec = new WalkerTestSpec(
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// "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference
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// + " -L 1:1-10,000,000 -B:omni,VCF " + validationDataLocation + file1
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// + " -B:hm3,VCF " + validationDataLocation + file2 + args,
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// 1,
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// Arrays.asList(md5));
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// executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
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// }
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//
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//
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// @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c", true); }
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// @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo", true); }
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// @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null", true); }
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// @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308", false); } // official project VCF files in tabix format
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//
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// @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12", false); }
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// @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d", false); }
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//
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// @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3", false); } // official project VCF files in tabix format
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// @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "802977fdfd2f4905b501bb06800f60af", false); } // official project VCF files in tabix format
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// @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a", false); }
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//
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// @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53", false); }
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//
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// @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48", true); }
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//
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// @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "902e541c87caa72134db6293fc46f0ad"); }
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// @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "f339ad4bb5863b58b9c919ce7d040bb9"); }
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//
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// @Test public void threeWayWithRefs() {
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// WalkerTestSpec spec = new WalkerTestSpec(
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// baseTestString(" -B:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
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// " -B:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
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// " -B:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
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// " -B:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
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// " -setKey centerSet" +
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// " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
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// " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
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// " -genotypeMergeOptions UNIQUIFY -L 1"),
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// 1,
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// Arrays.asList("a07995587b855f3214fb71940bf23c0f"));
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// executeTest("threeWayWithRefs", spec);
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// }
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// complex examples with filtering, indels, and multiple alleles
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@ -119,8 +119,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
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executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
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}
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@Test public void complexTestFull() { combineComplexSites("", "ec593a12f932af92f0f6e38cf9c4bc60"); }
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@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "977e27e407674e8a162f1773310294a5"); }
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@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "4bcab3ae334c718f4cf3203fe38d7ce6"); }
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@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "c70d0ccdb821921ea5bf7975364ad5a0"); }
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@Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
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@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "0db9ef50fe54b60426474273d7c7fa99"); }
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@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "d20acb3d53ba0a02ce92d540ebeda2a9"); }
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@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "8d1b3d120515f8b56b5a0d10bc5da713"); }
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}
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